top of page
mmu_circNusap1_501
Basic information of circular RNA
PanCircBase ID:
mmu_circNusap1_501
mm39_Chr. Position ID:
chr2|119465958|119474381|+
Gene name:
Nusap1
Transcript:
ENSMUST00000068225.15
CircRNA type:
Exonic circular (circ)RNA
Exon/Intron count:
4
Exon/intron indexes:
6,7,8,9
Exon/intron offsets:
0,2970,4099,8306
Genomic length:
8423
Exon/intron sizes in nt:
1,10,11,61,58,117
Flanking exon/introns:
chr2:119464299-119465958|chr2:119474381-119477570
Splice length:
501
Other database IDs:
CIRCpedia: MMU_CIRCpedia_4822, circAtlas: mmu-Nusap1_0002
Human Ortholog IDs:
Mature spliced Sequence:
ACTTTAAGAAGCTTCATGAGGCTCGTTTTAAGAAAATGGAATCCATTGATGAATATATTATGAGGAAAAAGAAACACCTTAAAGAACACAGTTCACTTAATGAACTAAAGCTTGACAAAAAAGGGATAGTGACCCCAGTTCCTCCAAGAGGAAGGCTCTCTGTACCCTGTACTCCTGCCAGGCAGCAGTGCCCACAAGGCCACTCAGCAACTAAAATGAATGTCAGGTTTTCAGCTGCTACTAAAGACAATGAACATAAGTGCTCACTGACCAAGACACCAGCCAGAAAGTCTCCACACGTGACTGCACCTGGGAGTGCTTCAAAAGGCCAGGCTGTGTTCAGGACACCCAAGTCAAAGGCCACTGAAAGGACTTCTATTGCAGTTATTACCCCTTTCAAGTTGATGACTGAAGCAACACAGACTCCAAGTTCTAGTAAGAAGCCAGTATTTGATCTCAAAGCAAGCTTGTCTCGTCCCCTCAACTACAAGCCACACAAAG
Divergent primers for circular RNA PCR
Primer Set-1
Forward primer
Tm
Reverse primer
Tm
Product size
AAGCAAGCTTGTCTCGTCCC
60.6
AAGTGAACTGTGTTCTTTAAGGTGT
59.06
140
Primer Set-2
Forward primer
Tm
Reverse primer
Tm
Product size
CAAAGCAAGCTTGTCTCGTCC
60.07
AGTGAACTGTGTTCTTTAAGGTGT
58.5
141
PCR template sequence:
TTGATGACTGAAGCAACACAGACTCCAAGTTCTAGTAAGAAGCCAGTATTTGATCTCAAAGCAAGCTTGTCTCGTCCCCTCAACTACAAGCCACACAAAGACTTTAAGAAGCTTCATGAGGCTCGTTTTAAGAAAATGGAATCCATTGATGAATATATTATGAGGAAAAAGAAACACCTTAAAGAACACAGTTCACTTAA
Note: Users can design additional primers for provided template sequence using Primer3 or NCBI primer-blast.
miRNAs associated with circular RNAs
No of miRNAs
6
Interacting miRNAs (#binding sites)
mmu-miR-200b-3p(1), mmu-miR-211-5p(1), mmu-miR-204-5p(1), mmu-miR-138-5p(1), mmu-miR-181b-5p(1), mmu-miR-181d-5p(1)
siRNAs for circular RNA silencing
Junction sequence
AAGCCACACAAAGACTTTAAGAAGCT
siRNA sets
CTTAAAGTCTTTGTGTGGC, TTCTTAAAGTCTTTGTGTG, TCTTAAAGTCTTTGTGTGG
Protein-coding potential of circular RNAs
CPAT analysis
CPAT ORF ID
CPAT Fickett
CPAT Hexamer
Coding probabilty
ORF length
CIRCNUSAP1_501_ORF_1
1.003
0.022644127
0.974968024
966
ORF sequence:
ATGGAATCCATTGATGAATATATTATGAGGAAAAAGAAACACCTTAAAGAACACAGTTCACTTAATGAACTAAAGCTTGACAAAAAAGGGATAGTGACCCCAGTTCCTCCAAGAGGAAGGCTCTCTGTACCCTGTACTCCTGCCAGGCAGCAGTGCCCACAAGGCCACTCAGCAACTAAAATGAATGTCAGGTTTTCAGCTGCTACTAAAGACAATGAACATAAGTGCTCACTGACCAAGACACCAGCCAGAAAGTCTCCACACGTGACTGCACCTGGGAGTGCTTCAAAAGGCCAGGCTGTGTTCAGGACACCCAAGTCAAAGGCCACTGAAAGGACTTCTATTGCAGTTATTACCCCTTTCAAGTTGATGACTGAAGCAACACAGACTCCAAGTTCTAGTAAGAAGCCAGTATTTGATCTCAAAGCAAGCTTGTCTCGTCCCCTCAACTACAAGCCACACAAAGACTTTAAGAAGCTTCATGAGGCTCGTTTTAAGAAAATGGAATCCATTGATGAATATATTATGAGGAAAAAGAAACACCTTAAAGAACACAGTTCACTTAATGAACTAAAGCTTGACAAAAAAGGGATAGTGACCCCAGTTCCTCCAAGAGGAAGGCTCTCTGTACCCTGTACTCCTGCCAGGCAGCAGTGCCCACAAGGCCACTCAGCAACTAAAATGAATGTCAGGTTTTCAGCTGCTACTAAAGACAATGAACATAAGTGCTCACTGACCAAGACACCAGCCAGAAAGTCTCCACACGTGACTGCACCTGGGAGTGCTTCAAAAGGCCAGGCTGTGTTCAGGACACCCAAGTCAAAGGCCACTGAAAGGACTTCTATTGCAGTTATTACCCCTTTCAAGTTGATGACTGAAGCAACACAGACTCCAAGTTCTAGTAAGAAGCCAGTATTTGATCTCAAAGCAAGCTTGTCTCGTCCCCTCAACTACAAGCCACACAAA
Peptide sequence:
MESIDEYIMRKKKHLKEHSSLNELKLDKKGIVTPVPPRGRLSVPCTPARQQCPQGHSATKMNVRFSAATKDNEHKCSLTKTPARKSPHVTAPGSASKGQAVFRTPKSKATERTSIAVITPFKLMTEATQTPSSSKKPVFDLKASLSRPLNYKPHKDFKKLHEARFKKMESIDEYIMRKKKHLKEHSSLNELKLDKKGIVTPVPPRGRLSVPCTPARQQCPQGHSATKMNVRFSAATKDNEHKCSLTKTPARKSPHVTAPGSASKGQAVFRTPKSKATERTSIAVITPFKLMTEATQTPSSSKKPVFDLKASLSRPLNYKPHK
IRESfinder result
IRESfinder score
0.633679534
IRES/non IRES
IRES
riboCIRC information
riboCIRC ID
NA
NA
Evidence
Peptide sequence:
NA
bottom of page